Query 036518
Match_columns 223
No_of_seqs 169 out of 822
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:51:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036518.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036518hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10343 RNA-binding protein Y 100.0 2.4E-29 5.3E-34 196.3 13.5 96 40-138 1-96 (97)
2 TIGR00253 RNA_bind_YhbY putati 100.0 3.5E-29 7.7E-34 194.5 13.5 86 42-128 1-86 (95)
3 PF01985 CRS1_YhbY: CRS1 / Yhb 100.0 2.1E-28 4.6E-33 184.7 10.8 84 42-126 1-84 (84)
4 COG1534 Predicted RNA-binding 100.0 6.1E-28 1.3E-32 188.5 12.3 97 41-139 1-97 (97)
5 KOG1990 Poly(A)-specific exori 99.9 7.4E-27 1.6E-31 226.8 8.2 184 3-186 343-531 (564)
6 KOG1990 Poly(A)-specific exori 98.0 6.3E-06 1.4E-10 81.2 4.7 117 15-132 148-267 (564)
7 COG1623 Predicted nucleic-acid 59.2 55 0.0012 31.3 8.1 47 95-144 104-152 (349)
8 PF13604 AAA_30: AAA domain; P 49.0 1.1E+02 0.0024 25.8 7.8 67 41-112 1-69 (196)
9 PRK13482 DNA integrity scannin 42.9 77 0.0017 30.4 6.5 48 95-145 98-147 (352)
10 PF02288 Dehydratase_MU: Dehyd 38.0 1.5E+02 0.0033 23.8 6.7 69 70-138 16-86 (112)
11 cd08616 PI-PLCXD1c Catalytic d 37.9 3.2E+02 0.0069 24.9 9.8 66 68-133 98-182 (290)
12 PF11471 Sugarporin_N: Maltopo 33.5 92 0.002 22.5 4.3 29 153-181 30-58 (60)
13 TIGR00730 conserved hypothetic 33.3 58 0.0013 27.8 3.8 32 49-80 118-149 (178)
14 PF04508 Pox_A_type_inc: Viral 32.0 60 0.0013 19.6 2.6 18 157-174 3-20 (23)
15 PF10369 ALS_ss_C: Small subun 31.8 1.2E+02 0.0027 22.2 4.8 39 85-127 6-44 (75)
16 cd08619 PI-PLCXDc_plant Cataly 31.7 1.3E+02 0.0028 28.1 5.9 69 68-136 92-175 (285)
17 PRK11895 ilvH acetolactate syn 31.5 1.6E+02 0.0034 25.1 6.0 74 43-127 53-126 (161)
18 KOG3119 Basic region leucine z 30.2 1.8E+02 0.004 26.4 6.6 36 158-193 232-267 (269)
19 PF15337 Vasculin: Vascular pr 29.9 47 0.001 26.5 2.4 47 34-81 26-72 (97)
20 PF03641 Lysine_decarbox: Poss 29.8 63 0.0014 25.9 3.2 34 49-82 75-109 (133)
21 PF11608 Limkain-b1: Limkain b 29.4 1.2E+02 0.0026 24.0 4.5 33 95-127 16-48 (90)
22 PF04568 IATP: Mitochondrial A 29.3 1.4E+02 0.0031 23.7 5.1 41 138-178 50-99 (100)
23 COG1098 VacB Predicted RNA bin 27.8 52 0.0011 27.5 2.4 26 68-93 38-63 (129)
24 KOG1257 NADP+-dependent malic 26.5 1.8E+02 0.0039 29.8 6.3 71 45-118 376-450 (582)
25 PRK12757 cell division protein 26.3 1E+02 0.0022 28.5 4.2 25 34-58 72-96 (256)
26 PF12207 DUF3600: Domain of un 25.5 5.3 0.00012 34.3 -3.8 71 33-103 65-141 (162)
27 COG2390 DeoR Transcriptional r 24.4 2.8E+02 0.0061 26.1 6.9 51 66-117 36-86 (321)
28 TIGR00285 DNA-binding protein 23.7 2.8E+02 0.006 21.7 5.6 54 59-112 2-55 (87)
29 PF09006 Surfac_D-trimer: Lung 23.6 1.5E+02 0.0033 20.7 3.8 28 155-183 6-33 (46)
30 PRK09423 gldA glycerol dehydro 23.1 3.7E+02 0.008 24.9 7.4 27 58-84 30-56 (366)
31 TIGR00119 acolac_sm acetolacta 23.0 2.1E+02 0.0046 24.2 5.3 74 43-127 52-125 (157)
32 PF14807 AP4E_app_platf: Adapt 22.0 3.6E+02 0.0077 21.5 6.1 51 73-123 7-58 (104)
33 PRK11608 pspF phage shock prot 21.6 3E+02 0.0065 25.2 6.4 50 45-94 17-69 (326)
34 cd08169 DHQ-like Dehydroquinat 20.9 1.9E+02 0.0042 26.8 5.1 50 58-107 24-78 (344)
35 COG0864 NikR Predicted transcr 20.6 30 0.00066 28.8 -0.2 44 73-116 87-130 (136)
36 cd08170 GlyDH Glycerol dehydro 20.1 4.3E+02 0.0092 24.2 7.1 28 58-85 23-50 (351)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.96 E-value=2.4e-29 Score=196.28 Aligned_cols=96 Identities=24% Similarity=0.399 Sum_probs=87.7
Q ss_pred CCCCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECC
Q 036518 40 HELTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGD 119 (223)
Q Consensus 40 e~LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~ 119 (223)
++||++||++||++||+|+|+|+||++||||+|+++++.+|++||||||++.+++++++++++++||+.+||++||+||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~ 80 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGK 80 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCc
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEecCCCCCCCCCCCC
Q 036518 120 DTVIFYRGKNYVQPEIMSP 138 (223)
Q Consensus 120 ~aII~YRgKny~~P~~l~P 138 (223)
+ +++||... .|.+..|
T Consensus 81 ~-~vlYR~~~--~~~i~lp 96 (97)
T PRK10343 81 T-LVLYRPTK--ERKISLP 96 (97)
T ss_pred E-EEEEecCC--CccCCCC
Confidence 5 55688753 3545444
No 2
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.96 E-value=3.5e-29 Score=194.54 Aligned_cols=86 Identities=24% Similarity=0.424 Sum_probs=82.6
Q ss_pred CCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeE
Q 036518 42 LTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDT 121 (223)
Q Consensus 42 LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~a 121 (223)
||++||++||++||+|+|+|+|||+||||+|+++++++|++||||||++.++++++++++|++||+.|||++||+||++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~- 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKT- 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccE-
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred EEEecCC
Q 036518 122 VIFYRGK 128 (223)
Q Consensus 122 II~YRgK 128 (223)
+++||+.
T Consensus 80 ~vlYR~~ 86 (95)
T TIGR00253 80 IVLYRPT 86 (95)
T ss_pred EEEEecC
Confidence 5568874
No 3
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.95 E-value=2.1e-28 Score=184.69 Aligned_cols=84 Identities=35% Similarity=0.531 Sum_probs=73.8
Q ss_pred CCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeE
Q 036518 42 LTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDT 121 (223)
Q Consensus 42 LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~a 121 (223)
||++|+++||+.||+|+|+|+|||+||||+|+++|+++|+.||||||+|.+++.++++++|+.||+.|||++|+++|++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~- 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRT- 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTE-
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCE-
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred EEEec
Q 036518 122 VIFYR 126 (223)
Q Consensus 122 II~YR 126 (223)
+|+||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 56687
No 4
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=6.1e-28 Score=188.50 Aligned_cols=97 Identities=27% Similarity=0.431 Sum_probs=89.9
Q ss_pred CCCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCe
Q 036518 41 ELTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDD 120 (223)
Q Consensus 41 ~LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~ 120 (223)
+||++|+++||+.||+++|+|+||++|||++|+.+|+++|++||||||++.+++.++++++|+.||+.+||.+||+||++
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~ 80 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred EEEEecCCCCCCCCCCCCc
Q 036518 121 TVIFYRGKNYVQPEIMSPI 139 (223)
Q Consensus 121 aII~YRgKny~~P~~l~P~ 139 (223)
+|+|| .+..++.+..|.
T Consensus 81 -~vlyr-~~~e~~~i~l~~ 97 (97)
T COG1534 81 -LVLYR-ESKEKRKISLPR 97 (97)
T ss_pred -EEEEe-cCcccccccCCC
Confidence 55688 566677776663
No 5
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.93 E-value=7.4e-27 Score=226.82 Aligned_cols=184 Identities=38% Similarity=0.583 Sum_probs=173.1
Q ss_pred HHhHHHHHHHHHHHHHHHHHHhccCCCCCCCCCC-CCCCCCCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHH
Q 036518 3 EALLFHNLRKASALNKFLSLRLKRYEVPKVQGPV-VKPHELTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWK 81 (223)
Q Consensus 3 ~~~~~~~~~~a~~k~~~l~~~L~~~e~~~~~~p~-~dpe~LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk 81 (223)
.++|.++++.++.|+++....|.+++.++.+... .+++.+|.+++.+++++|.++++++.+|++|+++|++.++|.||+
T Consensus 343 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk 422 (564)
T KOG1990|consen 343 TEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWK 422 (564)
T ss_pred HHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhh
Confidence 4789999999999999999999999998885544 999999999999999999999999999999999999999999999
Q ss_pred hCCeeEEEecCCCh-hhHHHHHHHHHHHhCCeeEEEECC---eEEEEecCCCCCCCCCCCCcccccHHHHHHHhHHHHHH
Q 036518 82 KHETVKVFCKPSKP-GQIHEFAEEIARLSGGIPIQIIGD---DTVIFYRGKNYVQPEIMSPIDTLSKKKALEKSKYEQSL 157 (223)
Q Consensus 82 ~hELVKVkv~~~~~-~d~keiAeeLa~~sGg~LVqvIG~---~aII~YRgKny~~P~~l~P~~lL~KrkAl~rs~~~q~~ 157 (223)
+||++||+|+.... .++++.|..++..+|+.+|+++.+ ++|++|||+||.+|..++|.++|+||+|+.+|+++|+.
T Consensus 423 ~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~ 502 (564)
T KOG1990|consen 423 SRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRK 502 (564)
T ss_pred hcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHH
Confidence 99999999999876 999999999999999999999854 35899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 036518 158 ESVRRFIAMAEKELELYYRHIALYGDPNN 186 (223)
Q Consensus 158 ~~l~~~i~~~e~~~~~~~~~~~~~~~~~~ 186 (223)
+++++||..++.+++++++++.....++.
T Consensus 503 ~a~~~~i~~~~~~~e~~~~~~~~~~~~~~ 531 (564)
T KOG1990|consen 503 EALKSHISDLEQEIEQLQASVEAMPAINK 531 (564)
T ss_pred HHHhhhcchhhhhHHHhhcchhccccccc
Confidence 99999999999999999999998766554
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.99 E-value=6.3e-06 Score=81.22 Aligned_cols=117 Identities=24% Similarity=0.348 Sum_probs=104.4
Q ss_pred HHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCC
Q 036518 15 ALNKFLSLRLKRYEVPKVQGPVVKPHELTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSK 94 (223)
Q Consensus 15 ~k~~~l~~~L~~~e~~~~~~p~~dpe~LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~ 94 (223)
.....+.+.++.|..|.+.-|...+..+|..+.-++|.+|....|++.+|.++.-.++.-.|..+|..|+..|+.+....
T Consensus 148 ~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~ 227 (564)
T KOG1990|consen 148 VDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGV 227 (564)
T ss_pred chhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcc
Confidence 34556778899999999999999999999999999999999999999999999999999999999999999998888765
Q ss_pred -hhhHHHHHHHH--HHHhCCeeEEEECCeEEEEecCCCCCC
Q 036518 95 -PGQIHEFAEEI--ARLSGGIPIQIIGDDTVIFYRGKNYVQ 132 (223)
Q Consensus 95 -~~d~keiAeeL--a~~sGg~LVqvIG~~aII~YRgKny~~ 132 (223)
......+|.++ -..+|+.||...+- .+++|+++++-.
T Consensus 228 ~~~~~~~~a~~l~~~~~tg~~lv~hN~~-~dv~y~~~~Fl~ 267 (564)
T KOG1990|consen 228 LETRKERMADELQELLLTGKVLVLHNKL-LDVMYRYKNFLS 267 (564)
T ss_pred hhhhccchHHHHHHHHhcCCeEEeeccc-eeeeeehhhccc
Confidence 34445677777 78899999999998 788999999977
No 7
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=59.22 E-value=55 Score=31.25 Aligned_cols=47 Identities=26% Similarity=0.335 Sum_probs=34.6
Q ss_pred hhhHHHHHHHHHHHhCCeeEEEE--CCeEEEEecCCCCCCCCCCCCcccccH
Q 036518 95 PGQIHEFAEEIARLSGGIPIQII--GDDTVIFYRGKNYVQPEIMSPIDTLSK 144 (223)
Q Consensus 95 ~~d~keiAeeLa~~sGg~LVqvI--G~~aII~YRgKny~~P~~l~P~~lL~K 144 (223)
...++..|+..|.+||..||++. -+++.+|+.+..|.-. -+..+|||
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS~rrNvITlY~~~~ky~L~---d~~~il~r 152 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAISERRNVITLYVGNLKYVLK---DSAFILSR 152 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEecccceEEEEecCeeeeec---ChHHHHHH
Confidence 56789999999999999999996 4667777777666321 23345654
No 8
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=49.00 E-value=1.1e+02 Score=25.82 Aligned_cols=67 Identities=13% Similarity=0.116 Sum_probs=46.5
Q ss_pred CCCHHHHHHHHHHhhcCCCeeee-CCCCCCHH-HHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCe
Q 036518 41 ELTGEERFYFKKMAQKRSNYVPI-GRRGVFGG-VILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGI 112 (223)
Q Consensus 41 ~LT~kERk~LRk~Ah~LKpvV~I-GK~GVTdg-VIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~ 112 (223)
.||++|+..++.+...-+.++.| |..|.--. ++..+..+|..++ .+|.+..... ..+..|...+|..
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT~----~Aa~~L~~~~~~~ 69 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPTN----KAAKELREKTGIE 69 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESSH----HHHHHHHHHHTS-
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCcH----HHHHHHHHhhCcc
Confidence 48999999999997776665555 99887554 4677899999987 7777776553 5666677777644
No 9
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=42.93 E-value=77 Score=30.45 Aligned_cols=48 Identities=25% Similarity=0.313 Sum_probs=33.7
Q ss_pred hhhHHHHHHHHHHHhCCeeEEEEC--CeEEEEecCCCCCCCCCCCCcccccHH
Q 036518 95 PGQIHEFAEEIARLSGGIPIQIIG--DDTVIFYRGKNYVQPEIMSPIDTLSKK 145 (223)
Q Consensus 95 ~~d~keiAeeLa~~sGg~LVqvIG--~~aII~YRgKny~~P~~l~P~~lL~Kr 145 (223)
...++.+|.-++++|||.+|.|.. +.+-+|+.|+-|. ...|..+++|-
T Consensus 98 ~GtRHRaA~gise~Tda~vIvVSee~g~Isl~~~g~~~~---~~d~~~l~~~a 147 (352)
T PRK13482 98 TGTRHRTAERVAKQTGVPVIAVSQRRNIITLYVGGLRYV---LEDIGVILSRA 147 (352)
T ss_pred CcHHHHHhhHHHHhcCCEEEEEecccCeEEEEECCEEEe---cCCHHHHHHHH
Confidence 567899999999999999999973 4455656665432 23455566654
No 10
>PF02288 Dehydratase_MU: Dehydratase medium subunit; InterPro: IPR003208 This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.; PDB: 2D0P_B 2D0O_D 1IWP_E 1MMF_B 1NBW_B 3AUJ_B 1UC5_B 1IWB_B 1EEX_E 1DIO_B ....
Probab=38.02 E-value=1.5e+02 Score=23.78 Aligned_cols=69 Identities=20% Similarity=0.181 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCee-EEEECC-eEEEEecCCCCCCCCCCCC
Q 036518 70 GGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIP-IQIIGD-DTVIFYRGKNYVQPEIMSP 138 (223)
Q Consensus 70 dgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~L-VqvIG~-~aII~YRgKny~~P~~l~P 138 (223)
..++.+|-.-++..++-=..+......|+..+|.+-+..|+.-| |.+... +++|-|+.-...+|....|
T Consensus 16 ~~~lrev~aGIEEEGip~~~~~~~~~~d~~~lA~~AA~~S~lgVGIGi~~~G~~vih~~~L~~~~pL~~~~ 86 (112)
T PF02288_consen 16 SDVLREVLAGIEEEGIPYRVVRVSDTSDVAFLAYQAARLSRLGVGIGIQSKGTIVIHYKDLPPLSPLFLFP 86 (112)
T ss_dssp HHHHHHHHHHHHCTT-EEEEEEECSSSSHHHHHHHHHHHSTTSEEEEE-TTSEEEEEETTS-TTS-SEEEE
T ss_pred hhHHHHHHhHhcccCCCeEEEeecCcccHHHHHHHHhhccCcceeEEEcCCCcEEEEcCCCCCCCCceecc
Confidence 46888888888877764333355556889999999999987543 555554 6899999887788887777
No 11
>cd08616 PI-PLCXD1c Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to
Probab=37.93 E-value=3.2e+02 Score=24.94 Aligned_cols=66 Identities=14% Similarity=0.184 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHHHHhC--CeeEEEecCC---ChhhHHHHHHHHHHHhCCeeEEE--------------ECCeEEEEecCC
Q 036518 68 VFGGVILNMHMHWKKH--ETVKVFCKPS---KPGQIHEFAEEIARLSGGIPIQI--------------IGDDTVIFYRGK 128 (223)
Q Consensus 68 VTdgVIeeI~~~Lk~h--ELVKVkv~~~---~~~d~keiAeeLa~~sGg~LVqv--------------IG~~aII~YRgK 128 (223)
-.+.++.+|..-+..| |+|-+.+... ..++-+.+...|....|..++.. .|..+||+|+..
T Consensus 98 ~~~~~L~~i~~fl~~~p~Evvil~~~~~~~~~~~~~~~l~~~l~~~fg~~l~~~~~~~~~~tL~~l~~~~krVIi~y~~~ 177 (290)
T cd08616 98 LVKEILEEINDFLTEHPKEVVILDFNHFYGMTEEDHEKLLKMIKSIFGKKLCPRDPDLLNVTLEYLWEKGYQVIVFYHDP 177 (290)
T ss_pred hHHHHHHHHHHHHHHCCCcEEEEEEEccCCCCHHHHHHHHHHHHHHhcccccCCCCCcCcCcHHHHHhCCCEEEEEECCC
Confidence 5567899999999976 9999999743 34556678888888887776542 167788889876
Q ss_pred CCCCC
Q 036518 129 NYVQP 133 (223)
Q Consensus 129 ny~~P 133 (223)
....|
T Consensus 178 ~~~~~ 182 (290)
T cd08616 178 VAKKP 182 (290)
T ss_pred ccccC
Confidence 54443
No 12
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=33.51 E-value=92 Score=22.49 Aligned_cols=29 Identities=17% Similarity=0.119 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 036518 153 YEQSLESVRRFIAMAEKELELYYRHIALY 181 (223)
Q Consensus 153 ~~q~~~~l~~~i~~~e~~~~~~~~~~~~~ 181 (223)
-+||+..|.+-+...|++....+.+..-|
T Consensus 30 iEqRLa~LE~rL~~ae~ra~~ae~~~~~~ 58 (60)
T PF11471_consen 30 IEQRLAALEQRLQAAEQRAQAAEARAKQA 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47999999999999999999888877654
No 13
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=33.29 E-value=58 Score=27.76 Aligned_cols=32 Identities=9% Similarity=0.244 Sum_probs=24.4
Q ss_pred HHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHH
Q 036518 49 YFKKMAQKRSNYVPIGRRGVFGGVILNMHMHW 80 (223)
Q Consensus 49 ~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~L 80 (223)
.+.+++.+-||++.++-+|.++.+++-++...
T Consensus 118 ~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~ 149 (178)
T TIGR00730 118 TWAQLGIHQKPIILFNVNGHFDGLVEWLKYSI 149 (178)
T ss_pred HHHHcCCCCCCEEEECCcchHHHHHHHHHHHH
Confidence 35566777889999888888888888777333
No 14
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=31.97 E-value=60 Score=19.62 Aligned_cols=18 Identities=22% Similarity=0.314 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 036518 157 LESVRRFIAMAEKELELY 174 (223)
Q Consensus 157 ~~~l~~~i~~~e~~~~~~ 174 (223)
++.++..|..||.+|+.-
T Consensus 3 ~~rlr~rI~dLer~L~~C 20 (23)
T PF04508_consen 3 MNRLRNRISDLERQLSEC 20 (23)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 467889999999998763
No 15
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=31.76 E-value=1.2e+02 Score=22.20 Aligned_cols=39 Identities=18% Similarity=0.226 Sum_probs=24.9
Q ss_pred eeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeEEEEecC
Q 036518 85 TVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDTVIFYRG 127 (223)
Q Consensus 85 LVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~aII~YRg 127 (223)
||||.+. ..+ ..-...|++..+|.+|.+-.++.+|=.=|
T Consensus 6 LiKV~~~---~~~-r~ei~~l~~~f~a~ivd~~~~~~iie~tG 44 (75)
T PF10369_consen 6 LIKVKAT---PEN-RSEILQLAEIFRARIVDVSPDSIIIELTG 44 (75)
T ss_dssp EEEEE-S---CHH-HHHHHHHHHHTT-EEEEEETTEEEEEEEE
T ss_pred EEEEECC---ccC-HHHHHHHHHHhCCEEEEECCCEEEEEEcC
Confidence 4566552 233 34456788899999999999877664443
No 16
>cd08619 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains u
Probab=31.65 E-value=1.3e+02 Score=28.13 Aligned_cols=69 Identities=10% Similarity=0.070 Sum_probs=50.4
Q ss_pred CCHHHHHHHHHHHHhC--CeeEEEecCCC-hhhHHHHHHHHHHHhCCeeEEEE------------CCeEEEEecCCCCCC
Q 036518 68 VFGGVILNMHMHWKKH--ETVKVFCKPSK-PGQIHEFAEEIARLSGGIPIQII------------GDDTVIFYRGKNYVQ 132 (223)
Q Consensus 68 VTdgVIeeI~~~Lk~h--ELVKVkv~~~~-~~d~keiAeeLa~~sGg~LVqvI------------G~~aII~YRgKny~~ 132 (223)
-.+.|+.++..-+..| |+|-+.++... .++..+....|.+..|..++... +..+|++|++..|..
T Consensus 92 ~~~dvL~~i~~FL~~hp~EvVIL~~k~ey~~~~~~~~~~~li~~lGd~l~~~~~~~~~~TL~eL~~krVIviy~~~~~~~ 171 (285)
T cd08619 92 PVDVVLNDIKRFLSETKSEFVILEIRTEYGHEDPPQFDLWLVEQLGDHLIHQDDSVFSKTLAELLPKRVICIWKPRKSPA 171 (285)
T ss_pred cHHHHHHHHHHHHHHCCCeEEEEEEeecccCCCchHHHHHHHHHhcchhccCCCccccccHHHHhCCcEEEEEcCCCCCc
Confidence 4588999999999876 99999997653 22333566777778888887542 344688899888887
Q ss_pred CCCC
Q 036518 133 PEIM 136 (223)
Q Consensus 133 P~~l 136 (223)
|..-
T Consensus 172 ~~~~ 175 (285)
T cd08619 172 PAVG 175 (285)
T ss_pred cCCC
Confidence 7654
No 17
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=31.48 E-value=1.6e+02 Score=25.07 Aligned_cols=74 Identities=12% Similarity=-0.011 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeEE
Q 036518 43 TGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDTV 122 (223)
Q Consensus 43 T~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~aI 122 (223)
++.....+.++-+++-+++.|---.=.+.|..+|- ||||.+.... ..-..+|++..+|.+|.+-.+..+
T Consensus 53 ~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~-------LiKv~~~~~~----r~~i~~i~~~f~a~ivdv~~~~~~ 121 (161)
T PRK11895 53 DEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELA-------LVKVRASGEN----RAEILRLADIFRAKIVDVTPESLT 121 (161)
T ss_pred CHHHHHHHHHHHhccccEEEEEecCCcchhheEEE-------EEEEECCccc----HHHHHHHHHHhCCEEEEecCCEEE
Confidence 46677788888888888877744222222222222 4555554322 345667888899999999888665
Q ss_pred EEecC
Q 036518 123 IFYRG 127 (223)
Q Consensus 123 I~YRg 127 (223)
|=-=|
T Consensus 122 iE~tG 126 (161)
T PRK11895 122 IEVTG 126 (161)
T ss_pred EEEeC
Confidence 53333
No 18
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=30.22 E-value=1.8e+02 Score=26.41 Aligned_cols=36 Identities=19% Similarity=0.209 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCccc
Q 036518 158 ESVRRFIAMAEKELELYYRHIALYGDPNNRNPMSIM 193 (223)
Q Consensus 158 ~~l~~~i~~~e~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (223)
++|+.-|.+|.+++..+.+.+..|..+...+...+.
T Consensus 232 ~~lr~~v~~l~~el~~~~~~~~~~~~~~~~~~~~~~ 267 (269)
T KOG3119|consen 232 EALRTQVEQLKKELATLRRLFLQLPKPGGALSSPEL 267 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccCCcccccc
Confidence 678888888888888888888888877666655443
No 19
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=29.93 E-value=47 Score=26.54 Aligned_cols=47 Identities=17% Similarity=0.223 Sum_probs=36.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHH
Q 036518 34 GPVVKPHELTGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWK 81 (223)
Q Consensus 34 ~p~~dpe~LT~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk 81 (223)
+-+....+||..|.+.|-....+|+ .--+||+|+-.+..-.+-..|.
T Consensus 26 eNde~~~PlTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr 72 (97)
T PF15337_consen 26 ENDENCLPLTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWR 72 (97)
T ss_pred cCCcccCcCcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhcccccc
Confidence 4456677899999999999999998 6778999987775555444454
No 20
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=29.79 E-value=63 Score=25.87 Aligned_cols=34 Identities=3% Similarity=0.139 Sum_probs=25.9
Q ss_pred HHHHHhhcCC-CeeeeCCCCCCHHHHHHHHHHHHh
Q 036518 49 YFKKMAQKRS-NYVPIGRRGVFGGVILNMHMHWKK 82 (223)
Q Consensus 49 ~LRk~Ah~LK-pvV~IGK~GVTdgVIeeI~~~Lk~ 82 (223)
.+.+++.+-+ |++.+|.+|-++++++.++.....
T Consensus 75 ~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 75 TLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 3466776777 999999999999999888754443
No 21
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=29.39 E-value=1.2e+02 Score=24.01 Aligned_cols=33 Identities=15% Similarity=0.408 Sum_probs=20.4
Q ss_pred hhhHHHHHHHHHHHhCCeeEEEECCeEEEEecC
Q 036518 95 PGQIHEFAEEIARLSGGIPIQIIGDDTVIFYRG 127 (223)
Q Consensus 95 ~~d~keiAeeLa~~sGg~LVqvIG~~aII~YRg 127 (223)
...++.=-..|++-+||.|+++.|++++|-|.+
T Consensus 16 ~~~I~~RL~qLsdNCGGkVl~v~~~tAilrF~~ 48 (90)
T PF11608_consen 16 PSSIKNRLRQLSDNCGGKVLSVSGGTAILRFPN 48 (90)
T ss_dssp HHHHHHHHHHHHHTTT--EEE--TT-EEEEESS
T ss_pred HHHHHHHHHHHhhccCCEEEEEeCCEEEEEeCC
Confidence 344455556777789999999999999886654
No 22
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=29.25 E-value=1.4e+02 Score=23.68 Aligned_cols=41 Identities=20% Similarity=0.329 Sum_probs=28.9
Q ss_pred CcccccHHHHHHHh-----HHHHHHHHHHHHHHH----HHHHHHHHHHHh
Q 036518 138 PIDTLSKKKALEKS-----KYEQSLESVRRFIAM----AEKELELYYRHI 178 (223)
Q Consensus 138 P~~lL~KrkAl~rs-----~~~q~~~~l~~~i~~----~e~~~~~~~~~~ 178 (223)
..+.++||+|-.-. .+.+.++.|+.++.+ -+++|+.+..++
T Consensus 50 ag~~f~krE~A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 50 AGGAFGKREAAQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hCCccchHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45789999885444 445566777777777 777888777665
No 23
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=27.78 E-value=52 Score=27.55 Aligned_cols=26 Identities=27% Similarity=0.327 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHHHhCCeeEEEecCC
Q 036518 68 VFGGVILNMHMHWKKHETVKVFCKPS 93 (223)
Q Consensus 68 VTdgVIeeI~~~Lk~hELVKVkv~~~ 93 (223)
|.+++|.+||++|.--+=|+|+|..-
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~i 63 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDI 63 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEee
Confidence 68999999999999999999999874
No 24
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=26.45 E-value=1.8e+02 Score=29.81 Aligned_cols=71 Identities=23% Similarity=0.220 Sum_probs=53.0
Q ss_pred HHHHHHHHHhhcCCCeeeeCCCCC----CHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEEC
Q 036518 45 EERFYFKKMAQKRSNYVPIGRRGV----FGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIG 118 (223)
Q Consensus 45 kERk~LRk~Ah~LKpvV~IGK~GV----TdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG 118 (223)
++-+-|-..-..+||.+.||-.|+ |+.|++.|..+ +|==-|--..|.....+-+|++.=.-|+|-.|=..|
T Consensus 376 ~~~~~L~e~V~~vKPtvLiG~S~~~g~Fteevl~~Ma~~---~erPiIFalSNPT~~aECtae~ay~~t~Gr~ifaSG 450 (582)
T KOG1257|consen 376 EEIKDLEEAVKEVKPTVLIGASGVGGAFTEEVLRAMAKS---NERPIIFALSNPTSKAECTAEQAYKWTKGRAIFASG 450 (582)
T ss_pred hHHHHHHHHHHhcCCcEEEecccCCccCCHHHHHHHHhc---CCCceEEecCCCccccccCHHHHhhhcCCcEEEecC
Confidence 345577778889999999999886 67777777765 444344556666677777888888888888777665
No 25
>PRK12757 cell division protein FtsN; Provisional
Probab=26.33 E-value=1e+02 Score=28.45 Aligned_cols=25 Identities=32% Similarity=0.502 Sum_probs=20.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCC
Q 036518 34 GPVVKPHELTGEERFYFKKMAQKRS 58 (223)
Q Consensus 34 ~p~~dpe~LT~kERk~LRk~Ah~LK 58 (223)
++...+..||++||..|-.+--.|+
T Consensus 72 ~~~~~~~qlt~Eqrqlleqmq~Dmr 96 (256)
T PRK12757 72 GEVNSPTQLTDEQRQLLEQMQADMR 96 (256)
T ss_pred CCcCCcccCCHHHHHHHHHHHHHHh
Confidence 4446777899999999999887774
No 26
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=25.52 E-value=5.3 Score=34.31 Aligned_cols=71 Identities=20% Similarity=0.136 Sum_probs=47.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCee------eeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHH
Q 036518 33 QGPVVKPHELTGEERFYFKKMAQKRSNYV------PIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAE 103 (223)
Q Consensus 33 ~~p~~dpe~LT~kERk~LRk~Ah~LKpvV------~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAe 103 (223)
.+-.+|.+.||..++..++++...|.|++ +--|.=+|+.-.+.--.+|-..|.|+|+.....+..+.++-+
T Consensus 65 ~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vlt~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~vpe 141 (162)
T PF12207_consen 65 KNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVLTQEEYDQYIEALMTYETVRVKTKSSGGITVEEVPE 141 (162)
T ss_dssp TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS-HHHHHHHHHHHHHHHHHHHHCT-SS---GGGS-H
T ss_pred cCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhcCHHHHHHHHHHHhhhheeeeeccCCCCCcHHhccH
Confidence 56789999999999999999999999985 223344666667777889999999999988665444444333
No 27
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=24.36 E-value=2.8e+02 Score=26.09 Aligned_cols=51 Identities=12% Similarity=0.114 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEE
Q 036518 66 RGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQII 117 (223)
Q Consensus 66 ~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvI 117 (223)
=||+..++..+=..-+...+|+|.+. ......-++.+.|.+..|-.=+.|+
T Consensus 36 LgiSR~~v~rlL~~Ar~~GiV~I~i~-~~~~~~~~Le~~L~~~fgL~~a~VV 86 (321)
T COG2390 36 LGISRATVSRLLAKAREEGIVKISIN-SPVEGCLELEQQLKERFGLKEAIVV 86 (321)
T ss_pred hCCCHHHHHHHHHHHHHCCeEEEEeC-CCCcchHHHHHHHHHhcCCCeEEEE
Confidence 47777777777777788888888887 4445555577777777665544443
No 28
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=23.73 E-value=2.8e+02 Score=21.72 Aligned_cols=54 Identities=17% Similarity=0.055 Sum_probs=44.0
Q ss_pred CeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCe
Q 036518 59 NYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGI 112 (223)
Q Consensus 59 pvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~ 112 (223)
+++.||+.++..-|++-+.+--+.-.=|.|+-.+.+-...=.+|+.|.......
T Consensus 2 ~~i~vG~KPvmnYVlavlt~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~ 55 (87)
T TIGR00285 2 NVVYIGNKPVMNYVLAVLTQLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPD 55 (87)
T ss_pred CEEEEcCCcHHHHHHHHHHHHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCC
Confidence 578999999999999888865455677888888888777788999999986543
No 29
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=23.61 E-value=1.5e+02 Score=20.70 Aligned_cols=28 Identities=14% Similarity=0.313 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 036518 155 QSLESVRRFIAMAEKELELYYRHIALYGD 183 (223)
Q Consensus 155 q~~~~l~~~i~~~e~~~~~~~~~~~~~~~ 183 (223)
|+.++|.-.+..|+...+.|+ .+.+|++
T Consensus 6 qQv~aL~~qv~~Lq~~fs~yK-Ka~lFp~ 33 (46)
T PF09006_consen 6 QQVEALQGQVQRLQAAFSQYK-KAELFPN 33 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-HHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHCCC
Confidence 445555555555555555542 3344443
No 30
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=23.07 E-value=3.7e+02 Score=24.89 Aligned_cols=27 Identities=19% Similarity=0.046 Sum_probs=15.6
Q ss_pred CCeeeeCCCCCCHHHHHHHHHHHHhCC
Q 036518 58 SNYVPIGRRGVFGGVILNMHMHWKKHE 84 (223)
Q Consensus 58 KpvV~IGK~GVTdgVIeeI~~~Lk~hE 84 (223)
+.++.|...++...+.+.+...|+.+.
T Consensus 30 ~~~livtd~~~~~~~~~~v~~~l~~~~ 56 (366)
T PRK09423 30 KRALVIADEFVLGIVGDRVEASLKEAG 56 (366)
T ss_pred CEEEEEEChhHHHHHHHHHHHHHHhCC
Confidence 344445555565666666666666653
No 31
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=23.03 E-value=2.1e+02 Score=24.16 Aligned_cols=74 Identities=12% Similarity=0.020 Sum_probs=44.1
Q ss_pred CHHHHHHHHHHhhcCCCeeeeCCCCCCHHHHHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeEE
Q 036518 43 TGEERFYFKKMAQKRSNYVPIGRRGVFGGVILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDTV 122 (223)
Q Consensus 43 T~kERk~LRk~Ah~LKpvV~IGK~GVTdgVIeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~aI 122 (223)
++.....+.++-+++-+++.|----=.+.+..+| -||||.+... + ..-..+|++..+|.+|.+-.+..+
T Consensus 52 d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl-------~LiKv~~~~~---~-r~~i~~i~~~f~a~ivdv~~~~~~ 120 (157)
T TIGR00119 52 DDKVLEQITKQLNKLVDVIKVSDLTESAIVEREL-------CLVKVSAPGE---G-RDEIIRLTNIFRGRIVDVSPDSYT 120 (157)
T ss_pred CHHHHHHHHHHHhcCccEEEEEecCCCcceeeEE-------EEEEEECCcc---C-HHHHHHHHHHhCCEEEEecCCEEE
Confidence 4666777777777777777764322122222221 2456655432 2 344567778899999999887665
Q ss_pred EEecC
Q 036518 123 IFYRG 127 (223)
Q Consensus 123 I~YRg 127 (223)
|=.=|
T Consensus 121 ie~tG 125 (157)
T TIGR00119 121 VEVTG 125 (157)
T ss_pred EEEcC
Confidence 54433
No 32
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=22.02 E-value=3.6e+02 Score=21.48 Aligned_cols=51 Identities=14% Similarity=0.222 Sum_probs=39.8
Q ss_pred HHHHHHHHHh-CCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEEECCeEEE
Q 036518 73 ILNMHMHWKK-HETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQIIGDDTVI 123 (223)
Q Consensus 73 IeeI~~~Lk~-hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqvIG~~aII 123 (223)
.++.-..|.. ..=+|+++...+.....++...+.+..+--+|++||+-.|.
T Consensus 7 TeeFG~~W~s~~~e~k~~l~~~~~~t~~~~l~~l~~~l~lh~VevIg~E~I~ 58 (104)
T PF14807_consen 7 TEEFGQLWLSFSNERKQNLPSSSQRTLPEFLQRLQQKLRLHVVEVIGNEGIF 58 (104)
T ss_pred HHHHHHHHHcCCCeEEEeccccCcCCHHHHHHHHHHhcCceEEEEeCcccee
Confidence 4566677776 45577888766667788899999999999999999975544
No 33
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=21.62 E-value=3e+02 Score=25.21 Aligned_cols=50 Identities=18% Similarity=0.194 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhcCCCeeeeCCCCCCHHHH-HHHHHHHH--hCCeeEEEecCCC
Q 036518 45 EERFYFKKMAQKRSNYVPIGRRGVFGGVI-LNMHMHWK--KHETVKVFCKPSK 94 (223)
Q Consensus 45 kERk~LRk~Ah~LKpvV~IGK~GVTdgVI-eeI~~~Lk--~hELVKVkv~~~~ 94 (223)
.-+..+++.|..-.|++..|-.|.--..+ ..||..-. ...+|.|.|..-+
T Consensus 17 ~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~ 69 (326)
T PRK11608 17 EVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALN 69 (326)
T ss_pred HHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCC
Confidence 45677888888889999999999988776 56776554 3579999999754
No 34
>cd08169 DHQ-like Dehydroquinate synthase-like which includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. Dehydroquinate synthase-like. This group contains dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. They exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes ne
Probab=20.92 E-value=1.9e+02 Score=26.79 Aligned_cols=50 Identities=12% Similarity=0.044 Sum_probs=29.5
Q ss_pred CCeeeeCCCCCCHHHHHHHHHHHHh-CCeeEEEecCC----ChhhHHHHHHHHHH
Q 036518 58 SNYVPIGRRGVFGGVILNMHMHWKK-HETVKVFCKPS----KPGQIHEFAEEIAR 107 (223)
Q Consensus 58 KpvV~IGK~GVTdgVIeeI~~~Lk~-hELVKVkv~~~----~~~d~keiAeeLa~ 107 (223)
+.++.|...++.+...+.+...++. +.+-.+.+... +.+.+.++++.+.+
T Consensus 24 ~k~livtd~~v~~~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~ 78 (344)
T cd08169 24 DQYFFISDSGVADLIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIA 78 (344)
T ss_pred CeEEEEECccHHHHHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHH
Confidence 4566666677777777778888876 45433444431 23455555555544
No 35
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=20.61 E-value=30 Score=28.82 Aligned_cols=44 Identities=23% Similarity=0.426 Sum_probs=37.4
Q ss_pred HHHHHHHHHhCCeeEEEecCCChhhHHHHHHHHHHHhCCeeEEE
Q 036518 73 ILNMHMHWKKHETVKVFCKPSKPGQIHEFAEEIARLSGGIPIQI 116 (223)
Q Consensus 73 IeeI~~~Lk~hELVKVkv~~~~~~d~keiAeeLa~~sGg~LVqv 116 (223)
+..+|.|++.+..+-+.+.++...++.++++.|....|...+..
T Consensus 87 iss~h~hl~~~~ClE~~vv~G~~~~i~~l~~~i~~~~gv~~~kl 130 (136)
T COG0864 87 ISSLHVHLDGDNCLEVIVVKGDSERIRELADKLRALRGVKHIKL 130 (136)
T ss_pred EEEeeEEcCCCceEEEEEEecCchhHHHHHHHHHhhcCeeEEEE
Confidence 34566788999999999999999999999999999988777664
No 36
>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=20.15 E-value=4.3e+02 Score=24.18 Aligned_cols=28 Identities=11% Similarity=-0.076 Sum_probs=18.5
Q ss_pred CCeeeeCCCCCCHHHHHHHHHHHHhCCe
Q 036518 58 SNYVPIGRRGVFGGVILNMHMHWKKHET 85 (223)
Q Consensus 58 KpvV~IGK~GVTdgVIeeI~~~Lk~hEL 85 (223)
+..+.|+..++..++.+.+...|+.+.+
T Consensus 23 ~r~livt~~~~~~~~~~~v~~~L~~~~i 50 (351)
T cd08170 23 KRALIIADEFVLDLVGAKIEESLAAAGI 50 (351)
T ss_pred CeEEEEECHHHHHHHHHHHHHHHHhCCC
Confidence 4555566666666777777777777643
Done!